Micro: Clean Up works wrong for menzen and methane

**Steps to Reproduce**
1. Load from file: [Clean up works wrong for menzen and methane.zip](https://github.com/epam/ketcher/files/13922957/Clean.up.works.wrong.for.menzen.and.methane.zip) (unzip first)
2. Press Clean Up button (Ctrl+Shift+L)

https://github.com/epam/Indigo/assets/26869421/7cc67e76-174d-4d97-913d-f32cd87a0f62

**Actual behavior**
System moves methane molecules to somewhere

**Expected behavior**
System remains everything in place

**Desktop (please complete the following information):**
- OS: Win10
- Browser Chrome Version 120.0.6099.130 (Official Build) (64-bit)

**Ketcher version** [e.g. v2.4.2].
Ketcher Version 2.18.0+dev.1 Build at 2024-01-11; 13:21:50
Indigo Toolkit Version 1.18.0-dev.4+1452.0-gaf1efce67-x86_64-linux-gnu-11.4.0